On 10 June 1948, the day after an attempt to take Latrun was performed by Yiftah and Harel brigades during the 1948 Arab–Israeli War, a battalion-size force of the Arab Legion, supported by irregulars and a dozen of armored cars, attacked the kibbutz. This was defended by 68 Haganah soldiers. After four hours of battle, the kibbutz fell. 39 defenders were killed, a dozen escaped, and the remaining were taken prisoner. Two Arab legionnaires were killed. At the evening, the kibbutz abandoned to the irregulars was taken back by two Palmach squads.[5]

Kibbutz Gezer in 1948

After the war it was rebuilt, but came apart in 1964 due to social difficulties. The current kibbutz was founded on 4 July 1974, by a Gar'in from North America.

Kibbutz Gezer Field is one of the few regulation baseball fields in Israel.[4] Construction of the field in 1983, funded by American donors, took six weeks. The first game was played within a few months. A backstop, covered benches for players and a refreshment stand were added at a later date. In 1989, a scoreboard and outfield fence were erected for the Maccabiah Games.[6]

Since 2014, a red-hair event has been held at the Kibbutz for the local Israeli red hair community.[7] However, the number of attendees has to be restricted due to the risk of rocket attacks, leading to anger in the red-hair community.[8]